Looks like there is a rom out there, I've never tried it myself. I don't think there were many changes other than the health/amrour tick down which was something like 1/2 points every second.
I'm working on a quake arcade machine and I came to realise those arcade controls are terrible for qukae. Instead I'm gonna go with embedding a part of the keyboard (wasd + some keys around and space) and a joystick for flying games (with 6 buttons on it) in it to act as a mouse
You've got to bear in mind the hammer arcade machines get once in location which is why they would have come up with this design, I think it would be fine in this situation.
Although I did play a 3rd person arena shooter in an arcade in roughly 1999 that used a a similar style to the Quake one but with a joystick instead of trackball/mouse.
joysticks suck too dude, look up the cab called WAR i think. Japan has this counter strike arcade varient called counter strike neo i think? and they have like 10 terminals using kb and mouse